- Author:
- Mabelle Lin <mlin865@aucklanduni.ac.nz>
- Date:
- 2022-08-31 15:08:23+12:00
- Desc:
- Add OrganScaffold.exf
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/663/rawfile/08dbb04bf5cbf689414636163b9523e757843f33/OrganScaffold-settings.json
{
"scaffold_settings": {
"deleteElementRanges": "",
"displayAxes": true,
"displayElementAxes": false,
"displayElementNumbers": false,
"displayLines": true,
"displayLinesExterior": false,
"displayMarkerPoints": false,
"displayModelRadius": false,
"displayNodeDerivativeLabels": [
"D1",
"D2",
"D3"
],
"displayNodeDerivatives": 0,
"displayNodeNumbers": false,
"displayNodePoints": false,
"displaySurfaces": true,
"displaySurfacesExterior": true,
"displaySurfacesTranslucent": true,
"displaySurfacesWireframe": false,
"modelCoordinatesField": "coordinates",
"scaffoldPackage": {
"_ScaffoldPackage": true,
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Central path": {
"_ScaffoldPackage": true,
"meshEdits": "EX Version: 3\nRegion: /\n!#nodeset nodes\nDefine node template: node1\nShape. Dimension=0\n#Fields=1\n1) coordinates, coordinate, rectangular cartesian, real, #Components=3\n x. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n y. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\n z. #Values=6 (value,d/ds1,d/ds2,d2/ds1ds2,d/ds3,d2/ds1ds3)\nNode template: node1\nNode: 1\n 7.080000000000000e+01 -1.700000000000000e+01 3.930000000000000e+01 -3.700000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 7.230000000000000e+01 -4.790000000000000e+01 -1.390000000000000e+01 -5.900000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.870000000000000e+01 4.500000000000000e+00\nNode: 2\n 5.110000000000000e+01 -2.230000000000000e+01 3.220000000000000e+01 -1.060000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n 3.070000000000000e+01 -3.490000000000000e+01 -2.050000000000000e+01 -7.200000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 4.140000000000000e+01 9.000000000000000e-01\nNode: 3\n 2.780000000000000e+01 -2.770000000000000e+01 1.870000000000000e+01 -1.510000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n 2.700000000000000e+00 -1.840000000000000e+01 -2.820000000000000e+01 -2.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 4.090000000000000e+01 -5.000000000000000e+00\nNode: 4\n -3.000000000000000e-01 -2.800000000000000e+01 2.300000000000000e+00 -1.290000000000000e+01 0.000000000000000e+00 0.000000000000000e+00\n -5.800000000000000e+00 -2.600000000000000e+00 -2.560000000000000e+01 4.600000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 3.230000000000000e+01 -9.400000000000000e+00\nNode: 5\n -2.650000000000000e+01 -2.060000000000000e+01 -7.500000000000000e+00 -6.400000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n -2.900000000000000e+00 8.000000000000000e+00 -1.920000000000000e+01 8.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 2.210000000000000e+01 -6.800000000000000e+00\nNode: 6\n -4.060000000000000e+01 -1.100000000000000e+01 -1.160000000000000e+01 -4.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 7.400000000000000e+00 1.250000000000000e+01 -1.020000000000000e+01 7.800000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.760000000000000e+01 -5.900000000000000e+00\nNode: 7\n -4.810000000000000e+01 -6.400000000000000e+00 -8.600000000000000e+00 4.000000000000000e-01 0.000000000000000e+00 0.000000000000000e+00\n 2.100000000000000e+01 1.570000000000000e+01 -3.500000000000000e+00 4.400000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.050000000000000e+01 -3.100000000000000e+00\nNode: 8\n -5.290000000000000e+01 -3.200000000000000e+00 -1.110000000000000e+01 -5.500000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 3.860000000000000e+01 1.930000000000000e+01 -1.900000000000000e+00 -1.100000000000000e+00 0.000000000000000e+00 0.000000000000000e+00\n 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.200000000000000e+01 6.100000000000000e+00\nGroup name: meshEdits\n!#nodeset nodes\nNode group:\n1..8\n",
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Coordinate dimensions": 3,
"D2 derivatives": true,
"D3 derivatives": true,
"Length": 1.0,
"Number of elements": 7
},
"scaffoldTypeName": "1D Path 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
],
"userAnnotationGroups": [
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "1",
"name": "fundus of stomach",
"ontId": "UBERON:0001160"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "2-3",
"name": "body of stomach",
"ontId": "UBERON:0001161"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "4-5",
"name": "pyloric antrum",
"ontId": "UBERON:0001165"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "6",
"name": "pyloric canal",
"ontId": "UBERON:0008858"
},
{
"_AnnotationGroup": true,
"dimension": 1,
"identifierRanges": "7",
"name": "duodenum",
"ontId": "UBERON:0002114"
}
]
},
"Circular muscle layer relative thickness": 0.25,
"Gastro-esophagal junction": {
"_ScaffoldPackage": true,
"rotation": [
0.0,
0.0,
0.0
],
"scaffoldSettings": {
"Number of elements across common": 2,
"Number of elements along": 2,
"Number of elements around ostium": 8,
"Number of elements through wall": 4,
"Number of vessels": 1,
"Ostium diameter": 25.0,
"Ostium inter-vessel distance": 0.0,
"Ostium inter-vessel height": 0.0,
"Ostium length": 15.0,
"Ostium wall relative thicknesses": [
0.55,
0.15,
0.25,
0.05
],
"Ostium wall thickness": 5.0,
"Outlet": false,
"Refine": false,
"Refine number of elements along": 4,
"Refine number of elements around": 4,
"Refine number of elements through wall": 1,
"Unit scale": 1.0,
"Use cross derivatives": false,
"Use linear through ostium wall": true,
"Use linear through vessel wall": true,
"Vessel angle 1 degrees": 0.0,
"Vessel angle 1 spread degrees": 0.0,
"Vessel angle 2 degrees": 0.0,
"Vessel end length factor": 1.0,
"Vessel inner diameter": 5.0,
"Vessel wall relative thicknesses": [
0.55,
0.15,
0.25,
0.05
],
"Vessel wall thickness": 3.0
},
"scaffoldTypeName": "3D Ostium 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
]
},
"Limiting ridge": false,
"Longitudinal muscle layer relative thickness": 0.05,
"Mucosa relative thickness": 0.55,
"Number of elements around duodenum": 16,
"Number of elements between cardia and duodenum": 6,
"Number of elements between fundus apex and cardia": 3,
"Number of elements through wall": 4,
"Refine": false,
"Refine number of elements surface": 4,
"Refine number of elements through wall": 1,
"Submucosa relative thickness": 0.15,
"Use linear through wall": true,
"Wall thickness": 5.0
},
"scaffoldTypeName": "3D Stomach 1",
"scale": [
1.0,
1.0,
1.0
],
"translation": [
0.0,
0.0,
0.0
]
}
},
"segmentation_data_settings": {
"displayDataContours": true,
"displayDataMarkerNames": true,
"displayDataMarkerPoints": true,
"displayDataPoints": false,
"displayDataRadius": false
}
}